pfrancav,
No, it is not necessary to uninstall your current version. You don't have to formally install the CVS version, as long as you call the executables with the correct paths.
For example, this one way to compile aMule and run aMule and amuleweb:
$ cd Directory_Where_You_Untarred_aMule_Sources
$ ./configure --with-denoise-level=3 --enable-debug --disable-optimize --enable-verbose --enable-amule-gui --enable-webserver --enable-ccache && make
$ src/amule &
$ src/webserver/src/amuleweb
Notice that running amuleweb automatically on startup should not be enabled on preferences, otherwise you will probably run the wrong executable.
Please, report your results! Good luck!